L9 Molecular Population Genetics 2 Flashcards Preview

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Flashcards in L9 Molecular Population Genetics 2 Deck (14)
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1
Q

Factors affecting LD

A

mutation, drift, limited recombination, demographic effects e,g, admixture, bottlenecks

There is LD between closely linked sites but no LD between distant sites as recombination has broken them up

2
Q

Admixture

A

The mixing of two genetically differentiated populations

Initially LD will be proportional to allele freq. differences between the two populations and is unrelated to the distance between markers

3
Q

Extended LD

A

Dependent on migration rate and recombination rate

4
Q

Five matings for moderns, Neanderthals

A

See OneNote

5
Q

LD - selective sweeps

A

See OneNote for diagram

  • LD can show which parts of the genome shows selection
  • selective sweeps for advantageous mutations can lead all the way to fixation
  • Selective sweep leaves certain footprints: No variation
6
Q

Reduction in genetic diversity as a consequence of selective sweep

A

See OneNote diagram
e.g 9 sites with no variation, sign of strong selective sweep
If demographic event, we might see signal across the whole genome

Limitations:
the wide the sweep, the easier to detect but the hard to identify THE selected site

7
Q

Selective sweep - Tajimas D

A

See OneNote diragram

If selective sweep, expect local excess of rare sites

Mutations arise over time, takes a while for it to drift away => more rare sites

In humans, it takes about 1MY for a neutral mutation to be fixed

8
Q

FOXP2

A

See OneNote

  • gene associated with speech and language
  • gene is highly conserved suggests lots of purifying selection acting on it
  • 2 aa changes but within humans there is a skew towards rare site, suggest selective sweep
  • Regions of human genome without denisovan or neanderthal genome - shown in pink, that is where the FOXP2 is
9
Q

Signs of a selective sweep - footprint

A

See OneNote

Left in the patterns of the nucleotide polymorphism:

  1. locally reduced heterozygosity
  2. skewed frequency spectrum
  3. Increased LD/haplotypes

From the footprint you can infer:

  • how recent?
  • how strong was the selective agent?
10
Q

Macpherson diagram 2007

A

See Macpherson 2007 diagram on OneNote

11
Q

CCRDELTA32

A

Case study
See OneNote
- estimate age of a variant by the length of the haplotype it occurs on
- allele with 32 nucleotide deletion provides some protection against AIDS
- rise of mutation to 13% in caucasians in 27 generations not due to positive selection, ancient DNA says the allele is older. Subsequent analysis of hapmap SNP data suggests demographic effect rather than a sweep

12
Q

To age a new allele

A
  • We assume the probability that a haplotype remains intact (P) equals the proportion of the original haplotype in current populations

P=(1-c)^G

13
Q

Hard sweep

A

single variant goes to fixation

the higher the integrative haplotype score, the stronger the selective sweep

14
Q

Lactase - selective sweep

A
  • Lactase region shows strong selective sweep in Europeans

- Lactase region has a very long haplotype